-
1
-
-
78651345652
-
The RCSB Protein Data Bank: Redesigned web site and web services
-
Rose,P.W., Beran,B., Bi,C., Bluhm,W.F., Dimitropoulos,D., Goodsell,D.S., Prlic,A., Quesada,M., Quinn,G.B., Westbrook,J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Rose, P.W.1
Beran, B.2
Bi, C.3
Bluhm, W.F.4
Dimitropoulos, D.5
Goodsell, D.S.6
Prlic, A.7
Quesada, M.8
Quinn, G.B.9
Westbrook, J.D.10
-
2
-
-
78651300218
-
PDBe: Protein Data Bank in Europe
-
Velankar,S., Alhroub,Y., Alili,A., Best,C., Boutselakis,H.C., Caboche,S., Conroy,M.J., Dana,J.M., van Ginkel,G., Golovin,A. et al. (2011) PDBe: Protein Data Bank in Europe. Nucleic Acids Res., 39, D402-D410.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Velankar, S.1
Alhroub, Y.2
Alili, A.3
Best, C.4
Boutselakis, H.C.5
Caboche, S.6
Conroy, M.J.7
Dana, J.M.8
Van Ginkel, G.9
Golovin, A.10
-
3
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
DOI 10.1038/nsb1203-980
-
Berman,H., Henrick,K. and Nakamura,H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980. (Pubitemid 37500485)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.12
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
4
-
-
38549138986
-
BioMagResBank
-
DOI 10.1093/nar/gkm957
-
Ulrich,E.L., Akutsu,H., Doreleijers,J.F., Harano,Y., Ioannidis,Y.E., Lin,J., Livny,M., Mading,S., Maziuk,D., Miller,Z. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408. (Pubitemid 351149757)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Ulrich, E.L.1
Akutsu, H.2
Doreleijers, J.F.3
Harano, Y.4
Ioannidis, Y.E.5
Lin, J.6
Livny, M.7
Mading, S.8
Maziuk, D.9
Miller, Z.10
Nakatani, E.11
Schulte, C.F.12
Tolmie, D.E.13
Kent, W.R.14
Yao, H.15
Markley, J.L.16
-
5
-
-
2442610955
-
DRESS: A Database of REfined Solution NMR Structures
-
DOI 10.1002/prot.20118
-
Nabuurs,S.B., Nederveen,A.J., Vranken,W., Doreleijers,J.F., Bonvin,A.M.J.J., Vuister,G.W., Vriend,G. and Spronk,C.A.E.M. (2004) DRESS: a database of REfined solution NMR structures. Proteins, 55, 483-486. (Pubitemid 38620072)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.3
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.J.J.5
Vuister, G.W.6
Vriend, G.7
Spronk, C.A.E.M.8
-
6
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
DOI 10.1002/prot.20408
-
Nederveen,A.J., Doreleijers,J.F., Vranken,W., Miller,Z., Spronk,C.A.E.M., Nabuurs,S.B., Güntert,P., Livny,M., Markley,J.L., Nilges,M. et al. (2005) RECOORD: a recalculated coordinate database of 500+proteins from the PDB using restraints from the BioMagResBank. Proteins, 59, 662-672. (Pubitemid 40695843)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.E.M.5
Nabuurs, S.B.6
Guntert, P.7
Livny, M.8
Markley, J.L.9
Nilges, M.10
Ulrich, E.L.11
Kaptein, R.12
Bonvin, A.M.J.J.13
-
7
-
-
79954611826
-
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures
-
Bernard,A., Vranken,W.F., Bardiaux,B., Nilges,M. and Malliavin,T.E. (2011) Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures. Proteins, 79, 1525-1537.
-
(2011)
Proteins
, vol.79
, pp. 1525-1537
-
-
Bernard, A.1
Vranken, W.F.2
Bardiaux, B.3
Nilges, M.4
Malliavin, T.E.5
-
8
-
-
66249103704
-
PDB-REDO: Automated re-refinement of X-ray structure models in the PDB
-
Joosten,R.P., Salzemann,J., Bloch,V., Stockinger,H., Berglund,A.-C., Blanchet,C., Bongcam-Rudloff,E., Combet,C., Costa,A.L.D., Deleage,G. et al. (2009) PDB-REDO: automated re-refinement of X-ray structure models in the PDB. J. Applied Crystallogr., 42, 376-384.
-
(2009)
J. Applied Crystallogr.
, vol.42
, pp. 376-384
-
-
Joosten, R.P.1
Salzemann, J.2
Bloch, V.3
Stockinger, H.4
Berglund, A.-C.5
Blanchet, C.6
Bongcam-Rudloff, E.7
Combet, C.8
Costa, A.L.D.9
Deleage, G.10
-
9
-
-
58849160465
-
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
-
Joosten,R., Womack,T., Vriend,G. and Bricogne,G. (2009) Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Cryst. D, 65, 176-185.
-
(2009)
Acta Cryst. D
, vol.65
, pp. 176-185
-
-
Joosten, R.1
Womack, T.2
Vriend, G.3
Bricogne, G.4
-
10
-
-
78649817914
-
On the complexity of Engh and Huber refinement restraints: The angle t as example
-
Touw,W.G. and Vriend,G. (2010) On the complexity of Engh and Huber refinement restraints: the angle t as example. Acta Crystallogr. D Biol. Crystallogr., 66, 1341-1350.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 1341-1350
-
-
Touw, W.G.1
Vriend, G.2
-
11
-
-
71049172008
-
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries
-
Doreleijers,J.F., Vranken,W.F., Schulte,C., Lin,J., Wedell,J.R., Penkett,C.J., Vuister,G.W., Vriend,G., Markley,J.L. and Ulrich,E.L. (2009) The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J. Biomol. NMR, 45, 389-396.
-
(2009)
J. Biomol. NMR
, vol.45
, pp. 389-396
-
-
Doreleijers, J.F.1
Vranken, W.F.2
Schulte, C.3
Lin, J.4
Wedell, J.R.5
Penkett, C.J.6
Vuister, G.W.7
Vriend, G.8
Markley, J.L.9
Ulrich, E.L.10
-
12
-
-
0030047142
-
Errors in protein structures
-
Hooft,R., Vriend,G., Sander,C. and Abola,E. (1996) Errors in protein structures. Nature, 381, 272.
-
(1996)
Nature
, vol.381
, pp. 272
-
-
Hooft, R.1
Vriend, G.2
Sander, C.3
Abola, E.4
-
13
-
-
0030339738
-
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
-
Laskowski,R., Rullmann,J. and MacArthur,M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 8, 477-486. (Pubitemid 126706801)
-
(1996)
Journal of Biomolecular NMR
, vol.8
, Issue.4
, pp. 477-486
-
-
Laskowski, R.A.1
Rullmann, J.A.C.2
MacArthur, M.W.3
Kaptein, R.4
Thornton, J.M.5
-
14
-
-
23144441604
-
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures
-
DOI 10.1007/s10858-005-2195-0
-
Doreleijers,J.F., Nederveen,A.J., Vranken,W. and Lin,J. (2005) BioMagResBank databases DOCR and FRED containing converted and Eltered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR, 32, 1-12. (Pubitemid 41086462)
-
(2005)
Journal of Biomolecular NMR
, vol.32
, Issue.1
, pp. 1-12
-
-
Doreleijers, J.F.1
Nederveen, A.J.2
Vranken, W.3
Lin, J.4
Bonvin, A.M.J.J.5
Kaptein, R.6
Markley, J.L.7
Ulrich, E.L.8
-
15
-
-
35848952931
-
A global analysis of NMR distance constraints from the PDB
-
Vranken,W. (2007) A global analysis of NMR distance constraints from the PDB. J. Biomol. NMR, 39, 303-314.
-
(2007)
J. Biomol. NMR
, vol.39
, pp. 303-314
-
-
Vranken, W.1
-
16
-
-
77955794370
-
Validation of archived chemical shifts through atomic coordinates
-
Rieping,W. and Vranken,W.F. (2010) Validation of archived chemical shifts through atomic coordinates. Proteins, 78, 2482-2489.
-
(2010)
Proteins
, vol.78
, pp. 2482-2489
-
-
Rieping, W.1
Vranken, W.F.2
-
17
-
-
0037354231
-
RefDB: A database of uniformly referenced protein chemical shifts
-
DOI 10.1023/A:1022836027055
-
Zhang,H., Neal,S. and Wishart,D. (2003) RefDB: a database of uniformly referenced protein chemical shifts. J. Biomol. NMR, 25, 173-195. (Pubitemid 36410583)
-
(2003)
Journal of Biomolecular NMR
, vol.25
, Issue.3
, pp. 173-195
-
-
Zhang, H.1
Neal, S.2
Wishart, D.S.3
-
18
-
-
68349093958
-
TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
-
Shen,Y., Delaglio,F., Cornilescu,G. and Bax,A. (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR, 44, 213-223.
-
(2009)
J. Biomol. NMR
, vol.44
, pp. 213-223
-
-
Shen, Y.1
Delaglio, F.2
Cornilescu, G.3
Bax, A.4
-
19
-
-
19444382397
-
The CCPN data model for NMR spectroscopy: Development of a software pipeline
-
DOI 10.1002/prot.20449
-
Vranken,W., Boucher,W., Stevens,T., Fogh,R., Pajon,A., Llinas,M., Ulrich,E.L., Markley,J.L., Ionides,J. and Laue,E. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687-696. (Pubitemid 40695845)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 687-696
-
-
Vranken, W.F.1
Boucher, W.2
Stevens, T.J.3
Fogh, R.H.4
Pajon, A.5
Llinas, M.6
Ulrich, E.L.7
Markley, J.L.8
Ionides, J.9
Laue, E.D.10
-
20
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
21
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
DOI 10.1016/0263-7855(96)00009-4
-
Koradi,R., Billeter,M. and Wüthrich,K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph, 14, 51-55. (Pubitemid 26152976)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.1
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wuthrich, K.3
-
22
-
-
0038407231
-
15N chemical shifts
-
DOI 10.1023/A:1023812930288
-
Neal,S., Nip,A., Zhang,H. and Wishart,D. (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR, 26, 215-240. (Pubitemid 36758442)
-
(2003)
Journal of Biomolecular NMR
, vol.26
, Issue.3
, pp. 215-240
-
-
Neal, S.1
Nip, A.M.2
Zhang, H.3
Wishart, D.S.4
-
23
-
-
0036814981
-
13C chemical shift statistics
-
DOI 10.1023/A:1020997118364
-
Schubert,M., Labudde,D., Oschkinat,H. and Schmieder,P. (2002) A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics. J. Biomol. NMR, 24, 149-154. (Pubitemid 35414678)
-
(2002)
Journal of Biomolecular NMR
, vol.24
, Issue.2
, pp. 149-154
-
-
Schubert, M.1
Labudde, D.2
Oschkinat, H.3
Schmieder, P.4
-
24
-
-
16344377050
-
Determinants of the endosomal localization of sorting nexin 1
-
DOI 10.1091/mbc.E04-06-0504
-
Zhong,Q., Watson,M.J., Lazar,C.S., Hounslow,A.M., Waltho,J.P. and Gill,G.N. (2005) Determinants of the endosomal localization of sorting nexin 1. Mol. Biol. Cell, 16, 2049-2057. (Pubitemid 40471970)
-
(2005)
Molecular Biology of the Cell
, vol.16
, Issue.4
, pp. 2049-2057
-
-
Zhong, Q.1
Watson, M.J.2
Lazar, C.S.3
Hounslow, A.M.4
Waltho, J.P.5
Gill, G.N.6
-
25
-
-
70349558318
-
Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts
-
Mulder,F. (2009) Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts. Chem. Bio. Chem., 10, 1477-1479.
-
(2009)
Chem. Bio. Chem.
, vol.10
, pp. 1477-1479
-
-
Mulder, F.1
-
26
-
-
79956116665
-
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
-
doi:10.1093/ database/baq021
-
Kinjo,A.R., Yamashita,R. and Nakamura,H. (2010) PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. Database, 2010, doi:10.1093/ database/baq021.
-
(2010)
Database, 2010
-
-
Kinjo, A.R.1
Yamashita, R.2
Nakamura, H.3
|